Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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http://plindenbaum.blo...
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Posts by Pierre Lindenbaum

<prev • 6,766 results • page 2 of 677 • next >
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Comment: C: Merging of sequence chunks
... change ` String n = S.getName();` to String n = S.getName(); int a=n.indexOf('@'); if(a!=-1) n=n.substring(0,a); ...
written 4 days ago by Pierre Lindenbaum102k
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Comment: C: Bedtools intersect returns 0, intersections present on IGV
... do file use the same chromosome notation ? are the files sorted ? are both files BED files ? ...
written 4 days ago by Pierre Lindenbaum102k
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Comment: C: Merging of sequence chunks
... what happened after you typed : make bioalcidaejdk ...
written 4 days ago by Pierre Lindenbaum102k
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Comment: C: How to retrieve direct children of a taxon through Entrez using taxon IDs
... how about using the taxdump file to get all the children of a given id ? ftp://ftp.ncbi.nih.gov/pub/taxonomy/ nodes.dmp --------- This file represents taxonomy nodes. The description for each node includes the following fields: tax_id -- node id in GenBank taxon ...
written 4 days ago by Pierre Lindenbaum102k
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Comment: C: Picard CollectHsMetrics malfunctioning
... check this please: https://github.com/broadinstitute/picard/issues/1003 ...
written 4 days ago by Pierre Lindenbaum102k
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Comment: C: bgzf_blocked error when using samtools
... error message is here: https://github.com/samtools/htslib/blob/44c6a36f2894b45ad6cb491833d27c6a2106410f/bgzf.c#L854 it an error with the way the file was compressed. the input or output bam file looks corrupted. try to check your input file is valid with gunzip -t input.bam && echo "V ...
written 4 days ago by Pierre Lindenbaum102k
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Answer: A: Merging of sequence chunks
... using bioalcidaejdk http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html and the following script: final Map> id2seqs= new HashMap<>(); stream().forEach(S->{ String n = S.getName(); if(!id2seqs.containsKey(n)) id2seqs.put(n,new ArrayList<>()); id2seqs.get(n ...
written 4 days ago by Pierre Lindenbaum102k
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Answer: A: How do I make a schema with all described variants within a gene?
... I wrote a uniprot->SVG interface for a colleague. http://lindenb.github.io/pages/uniprot/paintsvg.html you give a uniprot ID and fill a list of variant in a text area. You can later export and open it in inkscape. ![enter image description here][1] [1]: http://i.imgur.com/285L8uW.jpg ...
written 5 days ago by Pierre Lindenbaum102k
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Comment: C: Number of SNPs in VCF
... I don't understand your command, the word SIM001 will be only displayed in the CHROM header like a sample isn't it ? ...
written 5 days ago by Pierre Lindenbaum102k
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Answer: A: VarDict Amplicon-Aware Calling with barcoded seq data
... what's the output of awk -F '\t' '(int($3)chromStart) ...
written 5 days ago by Pierre Lindenbaum102k

Latest awards to Pierre Lindenbaum

Popular Question 3 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 4 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 4 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Scholar 4 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 6 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Appreciated 7 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 7 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Appreciated 7 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Chromosome Position From Ucsc Genome Browser
Scholar 13 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Getting A Vcf File From A Fasta Alignment
Scholar 14 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Popular Question 14 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Getting A Vcf File From A Fasta Alignment
Scholar 15 days ago, created an answer that has been accepted. For A: How many ID's exist in BioSample?
Appreciated 17 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Popular Question 18 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 20 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?
Popular Question 23 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Scholar 23 days ago, created an answer that has been accepted. For A: How Complex It Is To Analyze Ngs Data ?

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